High-Resolution Mapping of Interstitial Telomeric Repeats in Syrian Hamster Metaphase Chromosomes

Demin, S. Yu.; Pleskach, Nadezhda; Svetlova, Maria; Solovjeva, Ljudmila

doi:10.1159/000321676

Cited by 13 publications

(11 citation statements)

References 33 publications

(20 reference statements)

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“…The series of confocal sections were collected with the step size 0.25 μm, and maximal projections of the series were obtained. Negative (inverse) DAPI-banding pattern that is coincided with G-banding one was computer processed according to the protocol published [84]. Chromosome identification was going on with the help of images of individual G-banded mouse chromosomes with different level of compaction [41].…”

Section: Methodsmentioning

confidence: 99%

Tandemly repeated DNA families in the mouse genome

et al. 2011

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BackgroundFunctional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies.ResultsUsing a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites.To confirm our data, we next performed in situ hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to in silico predicted several extra-chromosomes were positive for TR by in situ analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions.ConclusionsChromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report new analysis that identified in silico and confirmed in situ 3/17 chromosome-specific probe TRPC-21-MM. Thus, the new classification had proven to be useful tool for continuation of genome study, while annotated TR can be the valuable source of cytogenetic probes for chromosome recognition.

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Section: Methodsmentioning

confidence: 99%

Tandemly repeated DNA families in the mouse genome

et al. 2011

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“…Confocal images were processed using ImageJ and Adobe Photoshop software as described elsewhere [57]. Briefly, color channels were split from the initial RGB image into separate images.…”

Section: Methodsmentioning

confidence: 99%

Improving the population genetics toolbox for the study of the African malaria vector Anopheles nili: microsatellite mapping to chromosomes

et al. 2011

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BackgroundAnopheles nili is a major vector of malaria in the humid savannas and forested areas of sub-Saharan Africa. Understanding the population genetic structure and evolutionary dynamics of this species is important for the development of an adequate and targeted malaria control strategy in Africa. Chromosomal inversions and microsatellite markers are commonly used for studying the population structure of malaria mosquitoes. Physical mapping of these markers onto the chromosomes further improves the toolbox, and allows inference on the demographic and evolutionary history of the target species.ResultsAvailability of polytene chromosomes allowed us to develop a map of microsatellite markers and to study polymorphism of chromosomal inversions. Nine microsatellite markers were mapped to unique locations on all five chromosomal arms of An. nili using fluorescent in situ hybridization (FISH). Probes were obtained from 300-483 bp-long inserts of plasmid clones and from 506-559 bp-long fragments amplified with primers designed using the An. nili genome assembly generated on an Illumina platform. Two additional loci were assigned to specific chromosome arms of An. nili based on in silico sequence similarity and chromosome synteny with Anopheles gambiae. Three microsatellites were mapped inside or in the vicinity of the polymorphic chromosomal inversions 2Rb and 2Rc. A statistically significant departure from Hardy-Weinberg equilibrium, due to a deficit in heterozygotes at the 2Rb inversion, and highly significant linkage disequilibrium between the two inversions, were detected in natural An. nili populations collected from Burkina Faso.ConclusionsOur study demonstrated that next-generation sequencing can be used to improve FISH for microsatellite mapping in species with no reference genome sequence. Physical mapping of microsatellite markers in An. nili showed that their cytological locations spanned the entire five-arm complement, allowing genome-wide inferences. The knowledge about polymorphic inversions and chromosomal locations of microsatellite markers has been useful for explaining differences in genetic variability across loci and significant differentiation observed among natural populations of An. nili.

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“…Images of DAPI-banded chromosomes were analyzed after processing in Adobe Photoshop 9.0 program as described previously [21]. Fluorescence intensity of FISH signals of individual TS and ITS was measured on images using ImageJ 1.43 (NIH, USA) program, and the relative fluorescence intensity of individual FISH signal was calculated as the ratio of its intensity and summarized fluorescence intensity of all signals on the metaphase chromosome spread.…”

Section: Methodsmentioning

confidence: 99%

“…Earlier, high-resolution DAPI-banding of Syrian hamster metaphase chromosomes combined with FISH allowed us to map large pericentromeric ITS to 4 pairs of autosomes (chromosome numbers: 2, 4 14, 20) and X-chromosome [21]. The goal of this study was to determine the distribution of ITS in all other chromosomes of Syrian hamster, estimate the relative lengths of all TS and ITS, and analyze their spatial organization in interphase nuclei.…”

Section: Introductionmentioning

confidence: 99%

Characterization of telomeric repeats in metaphase chromosomes and interphase nuclei of Syrian Hamster Fibroblasts

et al. 2012

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BackgroundRodents have been reported to contain large arrays of interstitial telomeric sequences (TTAGGG)n (ITS) located in pericentromeric heterochromatin. The relative sizes of telomeric sequences at the ends of chromosomes (TS) and ITS in Syrian hamster (Mesocricetus auratus) cells have not been evaluated yet, as well as their structural organization in interphase nuclei.ResultsFISH signal distribution analysis was performed on DAPI-banded metaphase chromosomes of Syrian hamster fibroblasts, and relative lengths of telomere signals were estimated. Besides well-distinguished FISH signals from ITS located on chromosomes ##2, 4, 14, 20 and X that we reported earlier, low-intensity FISH signals were visualized with different frequency of detection on all other metacentric chromosomes excluding chromosome #21. The analysis of 3D-distribution of TS in interphase nuclei demonstrated that some TS foci formed clearly distinguished associations (2–3 foci in a cluster) in the nuclei of cells subjected to FISH or transfected with the plasmid expressing telomeric protein TRF1 fused with GFP. In G0 and G1/early S-phase, the average total number of GFP-TRF1 foci per nucleus was less than that of PNA FISH foci in the corresponding cell cycle phases suggesting that TRF1 overexpression might contribute to the fusion of neighboring telomeres. The mean total number of GFP-TRF1 and FISH foci per nucleus was increased during the transition from G0 to G1/early S-phase that might be the consequence of duplication of some TS.ConclusionsThe relative lengths of TS in Syrian hamster cells were found to be moderately variable. All but one metacentric chromosomes contain ITS in pericentromeric heterochromatin indicating that significant rearrangements of ancestral genome occurred in evolution. Visualization of GFP-TRF1 fibrils that formed bridges between distinct telomeric foci allowed suggesting that telomere associations observed in interphase cells are reversible. The data obtained in the study provide the further insight in the structure and dynamics of telomeric sequences in somatic mammalian cells.

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High-Resolution Mapping of Interstitial Telomeric Repeats in Syrian Hamster Metaphase Chromosomes

Cited by 13 publications

References 33 publications

Tandemly repeated DNA families in the mouse genome

Tandemly repeated DNA families in the mouse genome

Improving the population genetics toolbox for the study of the African malaria vector Anopheles nili: microsatellite mapping to chromosomes

Characterization of telomeric repeats in metaphase chromosomes and interphase nuclei of Syrian Hamster Fibroblasts

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